biostudies-literatureFernandez-Gonzalez AJEuropean Union's Horizon Europe research and innovation programme under grant agreement No 101091255 (project Soil O-live), HE Soil Health mission239https://www.ebi.ac.uk/biostudies/studies/S-EPMC12659499biostudies-literatureUnknown13(1)<h4>Background</h4>The plant holobiont concept emphasizes the critical role of the microbiome in host plant health and resilience. Microbial communities have been shown to enhance plant resistance to abiotic stresses, such as drought and salinity, and to mitigate the impact of phytopathogens. Traditional microbiome engineering approaches face challenges due to the complexity of microbial interactions. To overcome these limitations, recent advances in transcriptomics and metataxonomics analyses enable the identification of microbiome-associated phenotypes, co-occurrence networks, and key host genes-microbiome interactions. We present a novel framework combining co-occurrence network analyses and transcriptome-microbiota correlations to identify keystone belowground microorganisms and host gMicrobiomeUnveiling essential host genes and keystone microorganisms of the olive tree holobiont linked to Verticillium wilt tolerance.PMC12659499HE/MISS-SOIL/0199Serrano ALuque FMercado-Blanco JFernandez-Lopez MFernandez-Gonzalez AJfalseUnveiling essential host genes and keystone microorganisms of the olive tree holobiont linked to Verticillium wilt tolerance.<h4>Background</h4>The plant holobiont concept emphasizes the critical role of the microbiome in host plant health and resilience. Microbial communities have been shown to enhance plant resistance to abiotic stresses, such as drought and salinity, and to mitigate the impact of phytopathogens. Traditional microbiome engineering approaches face challenges due to the complexity of microbial interactions. To overcome these limitations, recent advances in transcriptomics and metataxonomics analyses enable the identification of microbiome-associated phenotypes, co-occurrence networks, and key host genes-microbiome interactions. We present a novel framework combining co-occurrence network analyses and transcriptome-microbiota correlations to identify keystone belowground microorganisms and host g2025-01-01T00:00:00Z2025 Nov2026-06-08T04:47:31.093Z2026-06-08T03:08:22.462ZS-EPMC126594994129977510.1186/s40168-025-02216-5